UC San Diego

Many fundamental biological and physical processes taking place in benthic marine environments such as coral reefs, kelp forests, and sea grass beds occur at scales of a millimeter or less. For example, large reef ecosystems are cumulatively built by many coral colonies, these colonies are in turn composed of numerous individual coral polyps each on the order of one millimeter in diameter. The polyps feed on micro-scale plankton and get photosynthetic energy from single-celled symbiotic algae. Furthermore, micro-scale fluid motions and mixing surrounding coral polyps impact their ability to exchange critical dissolved solutes such as oxygen and nutrients with the surrounding water. Natural ocean environments are also complex and dynamic systems that are difficult or impossible to fully replicate in the lab. A distinct needthus exists for direct observations of important marine processes in situ. This thesis describes the development of novel underwater microscopic imaging and velocity measurement techniques for studying micro-scale biological and physical processes at the seafloor in the natural environment. These techniques are then applied specifically to study reef-building corals.

First, I describe the development and application of the Benthic Underwater Microscope (BUM). This diver-operated instrument performs non-invasive imaging of subjects on the seafloor in situ at nearly micrometer resolution. The instrument’s optical system combines a long working distance microscopic objective lens, a flexible electronically tunable lens, and focused reflectance illumination. The BUM was deployed in the ocean to study coordinated coral polyp behaviors, interspecies coral polyp competition, and algal colonization of bleached coral colonies.

Second, I modify the BUM to measure two-dimensional fluid velocities at micro-scales using micro-particle tracking velocimetry (μPTV). This is achieved by incorporating dark field illumination, rapid image pair acquisition, active particle seeding, and application of particle tracking algorithms. The system was used to measure fluid velocity fields at sub-millimeter scales around coral polyps in the ocean, and a viscous boundary layer was observed directly at the coral’s surface.

Finally, the underwater μPTV instrument was used to study spatiotemporal dynamics of fluid motion around individual coral polyps in situ. We measure shear stress at the coral’s surface and show waves periodically modulating the near-surface flow environment. The tools developed here provide a means to bring the lab into the ocean, offering a new window into important marine processes.